Add a from_ase_atoms() method to Structure

[Andrew-S-Rosen]

Summary

Adds a .from_ase_atoms() method to Structure to complement the pre-existing .to_ase_atoms(). In reality, this is just a shorthand for the adapter, but it felt awkward to have one direction but not the other.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

Summary by CodeRabbit

• New Features
  • Introduced a method for converting ase.Atoms to pymatgen Structure, enhancing interoperability between different scientific libraries.
• Tests
  • Added new assertions to ensure reliability of the new conversion functionality.

[coderabbitai]

Walkthrough

The recent update involves enhancing the pymatgen Structure class with a new method for converting ase.Atoms to pymatgen structures. This improvement is complemented by an additional assertion in the test suite to validate the conversion process.

Changes

File Path	Change Summary
pymatgen/core/structure.py	Added from_ase_atoms method to Structure class for converting ase.Atoms to pymatgen Structure.
tests/core/test_structure.py	Added assertion in test_to_ase_atoms to verify the new conversion method.

🐰✨
In the garden of code, where the data trees sway,
A new method hops in, oh what a day!
From ASE to pymatgen, a leap so bold,
Ensuring each atom is perfectly molded.
Cheers to the coders, with brains so bright,
For making our data dance just right! 🌟
🐇

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Recent Review Details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 6aa43fa and 803f315.

Files selected for processing (2)

• pymatgen/core/structure.py (1 hunks)
• tests/core/test_structure.py (2 hunks)

Files skipped from review as they are similar to previous changes (2)

• pymatgen/core/structure.py
• tests/core/test_structure.py

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[coderabbitai]

Actionable comments posted: 2

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 46b018d and f57d3be.

Files selected for processing (2)

• pymatgen/core/structure.py (1 hunks)
• tests/core/test_structure.py (1 hunks)

[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between f57d3be and 6aa43fa.

Files selected for processing (1)

• pymatgen/core/structure.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

• pymatgen/core/structure.py

[janosh]

nice one, thanks @Andrew-S-Rosen! 👍

[JaGeo]

Now I can simplify a lot of my lecture code. 😅
Thanks, @Andrew-S-Rosen !!

[Andrew-S-Rosen]

@shyuep --- just chiming in with another vote to remove coderabbit. It's super annoying. If not though, I'll just keep sass talking back to it until it spontaneously decides not to review anymore.

[shyuep]

@Andrew-S-Rosen Yes, it is just an experiment. But a question - are the proposed changes useful? I can understand the boiler is annoying and I can try to kill those off. Just wanted to know if there is any value or there is no value at all.

[Andrew-S-Rosen]

@Andrew-S-Rosen Yes, it is just an experiment. But a question - are the proposed changes useful? I can understand the boiler is annoying and I can try to kill those off. Just wanted to know if there is any value or there is no value at all.

@shyuep: In general, not really. I'm sure sometimes the proposed changes are useful, but the signal:noise ratio (both in terms of the chattiness and usefulness of the suggestions) is likely too low for contributors to get much value from it in my opinion. The only redeeming feature, in my view, is the edit of the original summary.

[shyuep]

@Andrew-S-Rosen I don't really care for the summary. Ok, I will disable it.

One thing - I am not sure I want a from_ase_atoms. I would prefer a simple Structure.from_object. this will support ASE atoms for now, but I am sure there are a lot of different formats we can convert a structure from.

[Andrew-S-Rosen]

@Andrew-S-Rosen I don't really care for the summary. Ok, I will disable it.

Much appreciated!

One thing - I am not sure I want a from_ase_atoms. I would prefer a simple Structure.from_object. this will support ASE atoms for now, but I am sure there are a lot of different formats we can convert a structure from.

This is a very good point. For instance, a Phonopy object might be relevant. In any case, I am fine with changes in this regard.